Interpretive Summary: Physical and genetic maps are roadmaps to the organization of genomes. The use of maps in crop improvement is essential for both maintaining crop quality and future improvements. A physical map of part of the wheat genome has been constructed. The current report describes the methods used to generate this physical map and focuses on part of one wheat chromosome, the end of the short arem of chromosome 3D. This map is compared to rice, barley, and the new model grass species Brachypodium. Results give insights into the evolution of this section of the wheat genome and information on the rates and distribution of chromosome recombination. The development of such physical maps will allow wheat breeders and other wheat scientists to design more rationale strategies for wheat improvement.

Technical Abstract:
Physical maps employing libraries of bacterial artificial chromosome (BAC) clones are essential for comparative genomics and sequencing of large and repetitive genomes such as those of wheat. We report the use of the Ae. tauschii, the diploid ancestor of the wheat D genome, for the construction of the physical map of a large distal region of chromosome arm 3DS. A physical map of 25.4 Mb was constructed by anchoring BAC clones of Ae. tauschii, with 85 EST on the Ae. tauschii and barley genetic maps. Aligned to the rice and Brachypodium distachyon genomic sequences and a high density SNP genetic map of barley, the mapped region is highly collinear to the orthologous chromosome 1 in rice, chromosome 2 in B. distachyon and chromosome 3H in barley. The recombination rate along the region in Ae. tauschii dropped from 2.19 cM/Mb in the distal region to 0.09 cM/Mb in the proximal region. The size of the gaps between contigs was evaluated by comparing the recombination rate along the map with the local recombination rates calculated on single contigs. Although the physical map reported here is for a portion of genome, it is nevertheless the first physical map using fingerprinting of a complete Triticeae genome, showing that global fingerprinting of the large plant genomes is capable of generating physical maps.